SoroushVahidi/scidocs huggingface dataset:
Clinicopathological Findings of Chronic Rejection in a Face Grafted Patient.
(2015)

BACKGROUND
Skin chronic rejection (CR) in vascularized composite allotransplantation has not been included in the Banff classification yet. We report a face-transplant patient who developed cutaneous clinicopathologic changes suggestive of CR.


METHODS
The recipient was a 27-year-old man with severe disfigurement of the lower face due to a pyrotechnic explosion. He received a facial allograft, including mandible, cheeks, lips, and chin, in November 2009. Immunosuppression included antithymocyte globulins and bone-marrow infusion then steroids, tacrolimus, and mycophenolate mofetil.


RESULTS
During the first posttransplant year the acute rejection episodes were characterized by reversible oedema and erythema of the graft. Subsequently, the patient developed primary asymptomatic Epstein-Barr virus (EBV) infection, followed by EBV+ B-cell lymphoma and hepatic EBV-associated posttransplant smooth muscle tumors; therefore, the immunosuppressive treatment was greatly reduced. Since the second posttransplant year, the allografted facial skin became progressively sclerotic and presented pigmented macules on a background of hypopigmentation and teleangiectasias, resulting in a poikilodermatous aspect. Skin biopsies showed epidermal atrophy, basal cell vacuolization, and diffuse dermal sclerosis in the absence of significant dermal cell infiltration. The dermal capillaries showed thickened walls and narrowed lumina, whereas the large vessels did not show significant alterations. Neither donor-specific antibodies nor vascular Cd4 deposits were detected.A dysfunction of the graft functions occurred. It was evidenced by a decrease in mouth opening and modification of some phonemes although lip closure was still possible allowing food intake.


CONCLUSIONS
This is the first report suggestive of CR in a face allotransplantation after immunosuppression minimization.
Multiparty Computation from Somewhat Homomorphic Encryption
(2011)

We propose a general multiparty computation protocol secure against an active adversary corrupting up to n−1 of the n players. The protocol may be used to compute securely arithmetic circuits over any finite field Fpk . Our protocol consists of a preprocessing phase that is both independent of the function to be computed and of the inputs, and a much more efficient online phase where the actual computation takes place. The online phase is unconditionally secure and has total computational (and communication) complexity linear in n, the number of players, where earlier work was quadratic in n. Moreover, the work done by each player is only a small constant factor larger than what one would need to compute the circuit in the clear. We show this is optimal for computation in large fields. In practice, for 3 players, a secure 64-bit multiplication can be done in 0.05 ms. Our preprocessing is based on a somewhat homomorphic cryptosystem. We extend a scheme by Brakerski et al., so that we can perform distributed decryption and handle many values in parallel in one ciphertext. The computational complexity of our preprocessing phase is dominated by the public-key operations, we need O(n/s) operations per secure multiplication where s is a parameter that increases with the security parameter of the cryptosystem. Earlier work in this model needed Ω(n) operations. In practice, the preprocessing prepares a secure 64-bit multiplication for 3 players in about 13 ms.
How To Exchange Secrets with Oblivious Transfer
(1981)

As this paper puts forward the notion of “Oblivious Transfers” and is a well-known and frequently cited paper, I felt I should typeset the manuscript, and here is the result. While typesetting, I tried to stick to the original manuscript as much as possible. However, there were some cases, such as a few typos or punctuation marks, which were changed. As in many papers on cryptography, Alice and Bob play the role of participants of the given cryptographic protocols. For the sake of readability, Alice’s and Bob’s messages were printed in red and blue ink, respectively. This work was carefully proofread by my colleague Y. Sobhdel (sobhdel@ce.sharif.edu). Thanks also to H. M. Moghaddam for mentioning a minor mistake in an earlier version. That said, I will be thankful if you inform me of any possible mistakes.
Proving the TLS Handshake Secure (As It Is)
(2014)

The TLS Internet Standard features a mixed bag of cryptographic algorithms and constructions, letting clients and servers negotiate their use for each run of the handshake. Although many ciphersuites are now well-understood in isolation, their composition remains problematic, and yet it is critical to obtain practical security guarantees for TLS. We experimentally confirm that all mainstream implementations of TLS share key materials between different algorithms, some of them of dubious strength. We outline attacks in their handling of resumption and renegotiation, stressing the need to model multiple related instances of the handshake. We study the provable security of the TLS handshake, as it is implemented and deployed. To capture the details of the standard and its main extensions, we rely on miTLS, a verified reference implementation of the protocol. miTLS inter-operates with mainstream browsers and servers for many protocol versions, configurations, and ciphersuites; and it provides application-level, provable security for some. We propose new agile security definitions and assumptions for the signatures, key encapsulation mechanisms (KEM), and key derivation algorithms used by the TLS handshake. By necessity, our definitions are stronger than those expected with simple modern protocols. To validate our model of key encapsulation, we prove that both RSA and Diffie-Hellman ciphersuites satisfy our definition for the KEM. In particular, we formalize the use of PKCS#1v1.5 encryption in TLS, including recommended countermeasures against Bleichenbacher attacks, and build a 3,000-line EasyCrypt proof of the security of the resulting master secret KEM against replayable chosen-ciphertext attacks under the assumption that ciphertexts are hard to re-randomize. Based on our new agile definitions, we construct a modular proof of security for the miTLS reference implementation of the handshake, including ciphersuite negotiation, key exchange, renegotiation, and resumption, treated as a detailed 3,600-line executable model. We present our main definitions, constructions, and proofs for an abstract model of the protocol, featuring series of related runs of the handshake with different ciphersuites. We also describe its refinement to account for the whole reference implementation, based on automated verification tools.
Founding Cryptography on Oblivious Transfer - Efficiently
(2008)

We present a simple and efficient compiler for transforming secure multi-party computation (MPC) protocols that enjoy security only with an honest majority into MPC protocols that guarantee security with no honest majority, in the oblivious-transfer (OT) hybrid model. Our technique works by combining a secure protocol in the honest majority setting with a protocol achieving only security against semi-honest parties in the setting of no honest majority. Applying our compiler to variants of protocols from the literature, we get several applications for secure two-party computation and for MPC with no honest majority. These include: • Constant-rate two-party computation in the OT-hybrid model. We obtain a statistically UC-secure two-party protocol in the OT-hybrid model that can evaluate a general circuit C of size s and depth d with a total communication complexity of O(s)+ poly(k, d, log s) and O(d) rounds. The above result generalizes to a constant number of parties. • Extending OTs in the malicious model. We obtain a computationally efficient protocol for generating many string OTs from few string OTs with only a constant amortized communication overhead compared to the total length of the string OTs. • Black-box constructions for constant-round MPC with no honest majority. We obtain general computationally UC-secure MPC protocols in the OT-hybrid model that use only a constant number of rounds, and only make a black-box access to a pseudorandom generator. This gives the first constant-round protocols for three or more parties that only make a black-box use of cryptographic primitives (and avoid expensive zero-knowledge proofs).
Better Key Sizes (and Attacks) for LWE-Based Encryption
(2010)

We analyze the concrete security and key sizes of theoretically sound lattice-based encryption schemes based on the “learning with errors” (LWE) problem. Our main contributions are: (1) a new lattice attack on LWE that combines basis reduction with an enumeration algorithm admitting a time/success tradeoff, which performs better than the simple distinguishing attack considered in prior analyses; (2) concrete parameters and security estimates for an LWE-based cryptosystem that is more compact and efficient than the well-known schemes from the literature. Our new key sizes are up to 10 times smaller than prior examples, while providing even stronger concrete security levels.
Time-series detection of perspiration as a liveness test in fingerprint devices
(2005)

Fingerprint scanners may be susceptible to spoofing using artificial materials, or in the worst case, dismembered fingers. An anti-spoofing method based on liveness detection has been developed for use in fingerprint scanners. This method quantifies a specific temporal perspiration pattern present in fingerprints acquired from live claimants. The enhanced perspiration detection algorithm presented here improves our previous work by including other fingerprint scanner technologies; using a larger, more diverse data set; and a shorter time window. Several classification methods were tested in order to separate live and spoof fingerprint images. The dataset included fingerprint images from 33 live subjects, 33 spoofs created with dental material and Play-Doh, and fourteen cadaver fingers. Each method had a different performance with respect to each scanner and time window. However, all the classifiers achieved approximately 90% classification rate for all scanners, using the reduced time window and the more comprehensive training and test sets.
Applying WinWin to Quality Requirements: A Case Study
(2001)

This paper describes the application of the WinWin paradigm to identify and resolve conflicts in a series of real-client, student-developer digital library projects. The paper is based on a case study of the statistical analysis of 15 projects and an in-depth analysis of one representative project. These analyses focus on the conflict resolution process, stakeholders' roles and their relationships to quality artifacts, and tool effectiveness. We show that stakeholders tend to accept satisfactory rather than optimal resolutions. Users and customers are more proactive in stating win conditions, whereas developers are more active in working toward resolutions. Further, we suggest that knowledge-based automated aids have potential to significantly enhance process effectiveness and efficiency. Finally, we conclude that such processes and tools have theoretical and practical implications in the quest for better software requirements elicitation.
Value Sensitive Design and Information Systems
(2004)

Value Sensitive Design is a theoretically grounded approach to the design of technology that accounts for human values in a principled and comprehensive manner throughout the design process. It employs an integrative and iterative tripartite methodology, consisting of conceptual, empirical, and technical investigations. We explicate Value Sensitive Design by drawing on three case studies. The first study concerns information and control of web browser cookies, implicating the value of informed consent. The second study concerns using high-definition plasma displays in an office environment to provide a window to the outside world, implicating the values of physical and psychological well-being and privacy in public spaces. The third study concerns an integrated land use, transportation, and environmental simulation system to support public deliberation and debate on major land use and transportation decisions, implicating the values of fairness, accountability, and support for the democratic process, as well as a highly diverse range of values that might be held by different stakeholders, such as environmental sustainability, opportunities for business expansion, or walkable neighborhoods. We conclude with direct and practical suggestions for how to engage in Value Sensitive Design.
Linear dimensionality reduction: survey, insights, and generalizations
(2015)

Linear dimensionality reduction methods are a cornerstone of analyzing high dimensional data, due to their simple geometric interpretations and typically attractive computational properties. These methods capture many data features of interest, such as covariance, dynamical structure, correlation between data sets, input-output relationships, and margin between data classes. Methods have been developed with a variety of names and motivations in many fields, and perhaps as a result the connections between all these methods have not been highlighted. Here we survey methods from this disparate literature as optimization programs over matrix manifolds. We discuss principal component analysis, factor analysis, linear multidimensional scaling, Fisher’s linear discriminant analysis, canonical correlations analysis, maximum autocorrelation factors, slow feature analysis, sufficient dimensionality reduction, undercomplete independent component analysis, linear regression, distance metric learning, and more. This optimization framework gives insight to some rarely discussed shortcomings of well-known methods, such as the suboptimality of certain eigenvector solutions. Modern techniques for optimization over matrix manifolds enable a generic linear dimensionality reduction solver, which accepts as input data and an objective to be optimized, and returns, as output, an optimal low-dimensional projection of the data. This simple optimization framework further allows straightforward generalizations and novel variants of classical methods, which we demonstrate here by creating an orthogonal-projection canonical correlations analysis. More broadly, this survey and generic solver suggest that linear dimensionality reduction can move toward becoming a blackbox, objective-agnostic numerical technology.
The complex dielectric constant of pure and sea water from microwave satellite observations
(2004)

We provide a new fit for the microwave complex dielectric constant of water in the salinity range between 0-40 ppt using two Debye relaxation wavelengths. For pure water, the fit is based on laboratory measurements in the temperature range between -20/spl deg/C and +40/spl deg/C including supercooled water and for frequencies up to 500 GHz. For sea water, our fit is valid for temperatures between -2/spl deg/C and +29/spl deg/C and for frequencies up to at least 90 GHz. At low frequencies, our new model is a modified version of the Klein-Swift model. We compare the results of the new fit with various other models and provide a validation using an extensive analysis of brightness temperatures from the Special Sensor Microwave Imager.
Concept-Based Information Retrieval Using Explicit Semantic Analysis
(2011)

Information retrieval systems traditionally rely on textual keywords to index and retrieve documents. Keyword-based retrieval may return inaccurate and incomplete results when different keywords are used to describe the same concept in the documents and in the queries. Furthermore, the relationship between these related keywords may be semantic rather than syntactic, and capturing it thus requires access to comprehensive human world knowledge. Concept-based retrieval methods have attempted to tackle these difficulties by using manually built thesauri, by relying on term cooccurrence data, or by extracting latent word relationships and concepts from a corpus. In this article we introduce a new concept-based retrieval approach based on Explicit Semantic Analysis (ESA), a recently proposed method that augments keyword-based text representation with concept-based features, automatically extracted from massive human knowledge repositories such as Wikipedia. Our approach generates new text features automatically, and we have found that high-quality feature selection becomes crucial in this setting to make the retrieval more focused. However, due to the lack of labeled data, traditional feature selection methods cannot be used, hence we propose new methods that use self-generated labeled training data. The resulting system is evaluated on several TREC datasets, showing superior performance over previous state-of-the-art results.
Measuring and Analyzing Write Amplification Characteristics of Solid State Disks
(2013)

Write amplification brings endurance challenges to NAND Flash-based solid state disks (SSDs) such as impacts upon their write endurance and lifetime. A large write amplification degrades program/erase cycles (P/Es) of NAND Flashes and reduces the endurance and performance of SSDs. The write amplification problem is mainly triggered by garbage collections, wear-leveling, metadata updates, and mapping table updates. Write amplification is defined as the ratio of data volume written by an SSD controller to data volume written by a host. In this paper, we propose a four-level model of write amplification for SSDs. The four levels considered in our model include the channel level, chip level, die level, and plane level. In light of this model, we design a method of analyzing write amplification of SSDs to trace SSD endurance and performance by incorporating the Ready/Busy (R/B) signal of NAND Flash. Our practical approach aims to measure the value of write amplification for an entire SSD rather than NAND Flashes. To validate our measurement technique and model, we implement a verified SSD (vSSD) system and perform a cross-comparison on a set of SSDs, which are stressed by micro-benchmarks and I/O traces. A new method for SSDs is adopted in our measurements to study the R/B signals of NAND Flashes in an SSD. Experimental results show that our model is accurate and the measurement technique is generally applicable to any SSDs.
Dietary phenolics: chemistry, bioavailability and effects on health.
(2009)

There is much epidemiological evidence that diets rich in fruit and vegetables can reduce the incidence of non-communicable diseases such as cardiovascular diseases, diabetes, cancer and stroke. These protective effects are attributed, in part, to phenolic secondary metabolites. This review summarizes the chemistry, biosynthesis and occurrence of the compounds involved, namely the C6-C3-C6 flavonoids-anthocyanins, dihydrochalcones, flavan-3-ols, flavanones, flavones, flavonols and isoflavones. It also includes tannins, phenolic acids, hydroxycinnamates and stilbenes and the transformation of plant phenols associated with food processing (for example, production of black tea, roasted coffee and matured wines), these latter often being the major dietary sources. Events that occur following ingestion are discussed, in particular, the deglycosylation, glucuronidation, sulfation and methylation steps that occur at various points during passage through the wall of the small intestine into the circulatory system and subsequent transport to the liver in the portal vein.We also summarise the fate of compounds that are not absorbed in the small intestine, but which pass into the large intestine where they are degraded by the colonic microflora to phenolic acids, which can be absorbed into the circulatory system and subjected to phase II metabolism prior to excretion. Initially, the protective effect of dietary phenolics was thought to be due to their antioxidant properties which resulted in a lowering of the levels of free radicals within the body.However, there is now emerging evidence that themetabolites of dietary phenolics,which appear in the circulatory systemin nmol/L to low mmol/L concentrations, exertmodulatory effects in cells through selective actions on different components of the intracellular signalling cascades vital for cellular functions such as growth, proliferation and apoptosis. In addition, the intracellular concentrations required to affect cell signalling pathways are considerably lower than those required to impact on antioxidant capacity. The mechanisms underlying these processes are discussed.
Visual Event Recognition in Videos by Learning from Web Data
(2010)

We propose a visual event recognition framework for consumer videos by leveraging a large amount of loosely labeled web videos (e.g., from YouTube). Observing that consumer videos generally contain large intraclass variations within the same type of events, we first propose a new method, called Aligned Space-Time Pyramid Matching (ASTPM), to measure the distance between any two video clips. Second, we propose a new transfer learning method, referred to as Adaptive Multiple Kernel Learning (A-MKL), in order to 1) fuse the information from multiple pyramid levels and features (i.e., space-time features and static SIFT features) and 2) cope with the considerable variation in feature distributions between videos from two domains (i.e., web video domain and consumer video domain). For each pyramid level and each type of local features, we first train a set of SVM classifiers based on the combined training set from two domains by using multiple base kernels from different kernel types and parameters, which are then fused with equal weights to obtain a prelearned average classifier. In A-MKL, for each event class we learn an adapted target classifier based on multiple base kernels and the prelearned average classifiers from this event class or all the event classes by minimizing both the structural risk functional and the mismatch between data distributions of two domains. Extensive experiments demonstrate the effectiveness of our proposed framework that requires only a small number of labeled consumer videos by leveraging web data. We also conduct an in-depth investigation on various aspects of the proposed method A-MKL, such as the analysis on the combination coefficients on the prelearned classifiers, the convergence of the learning algorithm, and the performance variation by using different proportions of labeled consumer videos. Moreover, we show that A-MKL using the prelearned classifiers from all the event classes leads to better performance when compared with A-MKL using the prelearned classifiers only from each individual event class.
Averaged Collapsed Variational Bayes Inference
(2017)

This paper presents the Averaged CVB (ACVB) inference and offers convergence-guaranteed and practically useful fast Collapsed Variational Bayes (CVB) inferences. CVB inferences yield more precise inferences of Bayesian probabilistic models than Variational Bayes (VB) inferences. However, their convergence aspect is fairly unknown and has not been scrutinized. To make CVB more useful, we study their convergence behaviors in a empirical and practical approach. We develop a convergence-guaranteed algorithm for any CVB-based inference called ACVB, which enables automatic convergence detection and frees non-expert practitioners from the difficult and costly manual monitoring of inference processes. In experiments, ACVB inferences are comparable to or better than those of existing inference methods and deterministic, fast, and provide easier convergence detection. These features are especially convenient for practitioners who want precise Bayesian inference with assured convergence.